SAXSdb — 5oxv

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H2B 1.1

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	DNA STRAND 1 (601-based sequence model) × 1 Histone H2A × 4 （Q6AZJ8） Histone H4 × 4 （P62799） Histone H3.2 × 4 （P84233） DNA STRAND 2 (601-based sequence model) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B11_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain H； PDBConstruct 1–126； UniProt 1–126 Author chain N； PDBConstruct 1–126； UniProt 1–126 Author chain R； PDBConstruct 1–126； UniProt 1–126

Histone H2A

Xenopus laevis

UniProt Q6AZJ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	DNA STRAND 1 (601-based sequence model) × 1 Histone H2B 1.1 × 4 （P02281） Histone H4 × 4 （P62799） Histone H3.2 × 4 （P84233） DNA STRAND 2 (601-based sequence model) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6AZJ8_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–130； UniProt 1–130 Author chain G； PDBConstruct 1–130； UniProt 1–130 Author chain M； PDBConstruct 1–130； UniProt 1–130 Author chain Q； PDBConstruct 1–130； UniProt 1–130

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	DNA STRAND 1 (601-based sequence model) × 1 Histone H2B 1.1 × 4 （P02281） Histone H2A × 4 （Q6AZJ8） Histone H3.2 × 4 （P84233） DNA STRAND 2 (601-based sequence model) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 2–103 Author chain F； PDBConstruct 1–102； UniProt 2–103 Author chain L； PDBConstruct 1–102； UniProt 2–103 Author chain P； PDBConstruct 1–102； UniProt 2–103

Histone H3.2

Xenopus laevis

UniProt P84233

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	DNA STRAND 1 (601-based sequence model) × 1 Histone H2B 1.1 × 4 （P02281） Histone H2A × 4 （Q6AZJ8） Histone H4 × 4 （P62799） DNA STRAND 2 (601-based sequence model) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_XENLA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136 Author chain K； PDBConstruct 1–135； UniProt 2–136 Author chain O； PDBConstruct 1–135； UniProt 2–136

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5oxv
Deposition date deposition_date	2017-09-07
Structure title title	Structure of the 4_601_157 tetranucleosome (C2 form)
Keywords keywords	nucleosome, histone, DNA, tetranucleosome, chromatin fiber, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5oxv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5oxv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5oxv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	72.76 Å
Rg (electron density)	72.35 Å
Total Rg	72.46 Å
Atom count	24648
Residues	2123
Excluded volume	398900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5oxv__assembly_1__model_1`	octadecameric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DNA STRAND 1 (601-based sequence model)
Molecular weight formula_weight	96886.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J
Atom count atom_count	24648

CTGCGCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGAGTACTGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGAGT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13979.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,N,H,D

MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H2A
Molecular weight formula_weight	14109.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q,M,G,C

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H4
Molecular weight formula_weight	11263.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,L,F,B

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Histone H3.2
Molecular weight formula_weight	15303.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,K,E,A

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA STRAND 2 (601-based sequence model)
Molecular weight formula_weight	96147.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATCCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCAGTACTCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCAGT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	348.839 Å
Unit-cell length b length_b	63.274 Å
Unit-cell length c length_c	271.361 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	6.721 Å
Low-resolution limit resolution_low	71.666 Å
R factor r_factor	0.3208
R_work r_work	0.3170
R_free r_free	0.3522

Structure of the 4_601_157 tetranucleosome (C2 form)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H2B 1.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3.2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5oxv__assembly_1__model_1

5oxv__assembly_1__model_1 | I(q)

5oxv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

7. Citations (1)